[R-sig-eco] Unifrac distance matrix with dbRDA in Vegan

[Jari Oksanen]

On 20/04/2012, at 17:29 PM, Migun Shakya wrote:

> Hi all,
>     There has been few publications in microbial ecology recently
> that have successfully used UniFrac distance matrix with dbRDA, but i
> have failed to find the clear idea on tools or R package that they
> have used. I know there is a capscale function in vegan that does
> dbRDA or CAP (Constrained Analysis of Principal Coordinates). I used
> this function to analyze my data with unifrac distance, but I am
> concerned as I couldnt find anything validating the use of unifrac
> distance metrics with capscale function of vegan.
Migee,

What do you think is a validation? 

As to dbRDA (capscale) or NMDS, these should should be valid with any dissimilarity measure, and unifrac distance is a dissimilarity measure. Sounds like perfectly valid to me.

By the way, I changed metaMDS function in vegan so that it easily accepts unifrac distances a couple of years ago after I was in a workshop with Susan Letcher, and she suggested I do this.

Cheers, Jari Oksanen

-- 
Jari Oksanen, Dept Biology, Univ Oulu, 90014 Finland